PDB Short entry for 2N3V HEADER PROTEIN BINDING 10-JUN-15 2N3V TITLE SOLUTION STRUCTURE OF THE RPN1 T1 SITE WITH K48-LINKED DIUBIQUITIN IN TITLE 2 THE EXTENDED BINDING MODE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26S PROTEASOME REGULATORY SUBUNIT RPN1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 482-612; COMPND 5 SYNONYM: HMG-COA REDUCTASE DEGRADATION PROTEIN 2, PROTEASOME NON- COMPND 6 ATPASE SUBUNIT 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBIQUITIN-60S RIBOSOMAL PROTEIN L40; COMPND 10 CHAIN: B, C; COMPND 11 FRAGMENT: UNP RESIDUES 1-76; COMPND 12 SYNONYM: CEP52, UBIQUITIN A-52 RESIDUE RIBOSOMAL PROTEIN FUSION COMPND 13 PRODUCT 1, UBIQUITIN, 60S RIBOSOMAL PROTEIN L40; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: RPN1, HRD2, NAS1, RPD1, YHR027C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: UBA52, UBCEP2; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR X.CHEN,K.J.WALTERS REVDAT 3 14-JUN-23 2N3V 1 REMARK LINK REVDAT 2 23-MAR-16 2N3V 1 JRNL REVDAT 1 24-FEB-16 2N3V 0 JRNL AUTH Y.SHI,X.CHEN,S.ELSASSER,B.B.STOCKS,G.TIAN,B.H.LEE,Y.SHI, JRNL AUTH 2 N.ZHANG,S.A.DE POOT,F.TUEBING,S.SUN,J.VANNOY,S.G.TARASOV, JRNL AUTH 3 J.R.ENGEN,D.FINLEY,K.J.WALTERS JRNL TITL RPN1 PROVIDES ADJACENT RECEPTOR SITES FOR SUBSTRATE BINDING JRNL TITL 2 AND DEUBIQUITINATION BY THE PROTEASOME. JRNL REF SCIENCE V. 351 2016 JRNL REFN ESSN 1095-9203 JRNL PMID 26912900 JRNL DOI 10.1126/SCIENCE.AAD9421 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N3V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000104388. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM [U-100% 15N] PROTEIN_1, REMARK 210 0.04-1.2 MM PROTEIN_2, 50 MM REMARK 210 HEPES, 50 MM SODIUM CHLORIDE, 1 REMARK 210 MM EDTA, 2 MM DTT, 0.1 % SODIUM REMARK 210 AZIDE, 95% H2O/5% D2O; 0.08-0.3 REMARK 210 MM PROTEIN_1, 0.3 MM [U-100% 15N] REMARK 210 PROTEIN_2, 50 MM HEPES, 50 MM REMARK 210 SODIUM CHLORIDE, 1 MM EDTA, 2 MM REMARK 210 DTT, 0.1 % SODIUM AZIDE, 95% H2O/ REMARK 210 5% D2O; 0.06-0.5 MM PROTEIN_1, REMARK 210 0.5 MM [U-13C] PROTEIN_2, 50 MM REMARK 210 HEPES, 50 MM SODIUM CHLORIDE, 1 REMARK 210 MM EDTA, 2 MM DTT, 0.1 % SODIUM REMARK 210 AZIDE, 100% D2O; 0.6 MM [U-13C] REMARK 210 PROTEIN_1, 0.6 MM PROTEIN_2, 50 REMARK 210 MM HEPES, 50 MM SODIUM CHLORIDE, REMARK 210 1 MM EDTA, 2 MM DTT, 0.1 % REMARK 210 SODIUM AZIDE, 100% D2O; 0.5 MM REMARK 210 PROTEIN_ 1, 0.5 MM [U-13C] REMARK 210 PROTEIN_2, 50 MM HEPES, 50 MM REMARK 210 SODIUM CHLORIDE, 1 MM EDTA, 2 MM REMARK 210 DTT, 0.1 % SODIUM AZIDE, 100% REMARK 210 D2O; 0.6 MM [U-13C] PROTEIN_1, REMARK 210 0.12-0.6 MM PROTEIN_2, 50 MM REMARK 210 HEPES, 50 MM SODIUM CHLORIDE, 1 REMARK 210 MM EDTA, 2 MM DTT, 0.1 % SODIUM REMARK 210 AZIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 13C-HALF FILTER REMARK 210 NOESY; 4D HMQC-NOESY-HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, XEASY, X-PLOR REMARK 210 NIH NIH, TALOS, PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 THR A 483 88.38 -66.03 REMARK 500 1 PHE A 497 -73.90 -42.17 REMARK 500 1 SER A 500 35.64 -167.29 REMARK 500 1 LYS A 501 99.46 62.77 REMARK 500 1 ALA A 514 -37.88 -153.71 REMARK 500 1 THR A 516 -45.94 -171.41 REMARK 500 1 ASP A 517 -76.21 -146.01 REMARK 500 1 LEU A 518 149.43 55.03 REMARK 500 1 GLU A 521 -80.59 -49.81 REMARK 500 1 ALA A 531 -72.10 -56.25 REMARK 500 1 VAL A 533 -73.66 -61.20 REMARK 500 1 PHE A 534 29.54 -73.11 REMARK 500 1 ALA A 555 5.46 57.34 REMARK 500 1 LEU A 558 -9.83 -54.04 REMARK 500 1 TRP A 562 -9.11 -178.17 REMARK 500 1 MET A 575 12.63 -178.09 REMARK 500 1 GLN A 577 -35.17 -172.74 REMARK 500 1 GLU A 579 37.39 25.61 REMARK 500 1 ILE A 591 68.02 -102.93 REMARK 500 1 GLU A 592 -168.12 60.70 REMARK 500 1 PRO A 594 -158.14 -75.06 REMARK 500 1 MET A 595 4.41 -64.39 REMARK 500 1 LEU A 602 -73.84 -44.13 REMARK 500 1 ALA A 607 -87.52 -172.07 REMARK 500 1 THR A 611 -5.91 -167.65 REMARK 500 1 LEU B 8 44.45 -72.73 REMARK 500 1 THR B 9 -43.98 -143.73 REMARK 500 1 GLU B 34 -108.54 -81.76 REMARK 500 1 ASP B 39 21.99 -63.88 REMARK 500 1 GLN B 40 48.81 -151.85 REMARK 500 1 ALA B 46 27.46 49.05 REMARK 500 1 ASP B 52 178.40 -54.58 REMARK 500 1 ARG B 54 166.23 -41.61 REMARK 500 1 GLN B 62 -160.23 -77.59 REMARK 500 1 ARG B 72 89.44 -68.47 REMARK 500 1 LEU B 73 78.53 52.35 REMARK 500 1 GLU C 34 -101.35 -88.86 REMARK 500 1 ASP C 39 28.22 -70.05 REMARK 500 1 GLN C 40 47.43 -155.00 REMARK 500 1 LYS C 48 -142.86 -146.32 REMARK 500 1 ARG C 54 161.99 -39.60 REMARK 500 1 LEU C 56 3.18 -64.24 REMARK 500 1 TYR C 59 -9.79 -141.47 REMARK 500 1 ILE C 61 106.92 -58.65 REMARK 500 1 GLN C 62 -157.72 -84.54 REMARK 500 1 LEU C 73 164.85 60.65 REMARK 500 2 ALA A 489 -70.97 -75.86 REMARK 500 2 LEU A 491 -75.02 -57.92 REMARK 500 2 SER A 500 -82.41 -174.42 REMARK 500 2 THR A 516 -57.76 -169.17 REMARK 500 REMARK 500 THIS ENTRY HAS 470 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 553 0.31 SIDE CHAIN REMARK 500 1 ARG A 564 0.12 SIDE CHAIN REMARK 500 1 ARG B 42 0.31 SIDE CHAIN REMARK 500 1 ARG B 54 0.18 SIDE CHAIN REMARK 500 1 ARG B 72 0.13 SIDE CHAIN REMARK 500 1 ARG B 74 0.24 SIDE CHAIN REMARK 500 1 ARG C 42 0.12 SIDE CHAIN REMARK 500 1 ARG C 54 0.29 SIDE CHAIN REMARK 500 1 ARG C 72 0.19 SIDE CHAIN REMARK 500 1 ARG C 74 0.30 SIDE CHAIN REMARK 500 2 ARG A 553 0.28 SIDE CHAIN REMARK 500 2 ARG A 564 0.11 SIDE CHAIN REMARK 500 2 ARG B 42 0.30 SIDE CHAIN REMARK 500 2 ARG B 54 0.29 SIDE CHAIN REMARK 500 2 ARG B 72 0.29 SIDE CHAIN REMARK 500 2 ARG C 42 0.12 SIDE CHAIN REMARK 500 2 ARG C 54 0.29 SIDE CHAIN REMARK 500 2 ARG C 72 0.27 SIDE CHAIN REMARK 500 2 ARG C 74 0.25 SIDE CHAIN REMARK 500 3 ARG A 564 0.09 SIDE CHAIN REMARK 500 3 ARG B 42 0.26 SIDE CHAIN REMARK 500 3 ARG B 54 0.24 SIDE CHAIN REMARK 500 3 ARG B 72 0.31 SIDE CHAIN REMARK 500 3 ARG B 74 0.27 SIDE CHAIN REMARK 500 3 ARG C 42 0.23 SIDE CHAIN REMARK 500 3 ARG C 54 0.17 SIDE CHAIN REMARK 500 3 ARG C 72 0.28 SIDE CHAIN REMARK 500 3 ARG C 74 0.20 SIDE CHAIN REMARK 500 4 ARG A 553 0.19 SIDE CHAIN REMARK 500 4 ARG A 564 0.31 SIDE CHAIN REMARK 500 4 ARG B 42 0.28 SIDE CHAIN REMARK 500 4 ARG B 54 0.11 SIDE CHAIN REMARK 500 4 ARG B 72 0.23 SIDE CHAIN REMARK 500 4 ARG B 74 0.31 SIDE CHAIN REMARK 500 4 ARG C 42 0.22 SIDE CHAIN REMARK 500 4 ARG C 54 0.31 SIDE CHAIN REMARK 500 4 ARG C 72 0.14 SIDE CHAIN REMARK 500 4 ARG C 74 0.29 SIDE CHAIN REMARK 500 5 ARG A 553 0.30 SIDE CHAIN REMARK 500 5 ARG A 564 0.23 SIDE CHAIN REMARK 500 5 ARG B 42 0.30 SIDE CHAIN REMARK 500 5 ARG B 54 0.29 SIDE CHAIN REMARK 500 5 ARG B 72 0.29 SIDE CHAIN REMARK 500 5 ARG B 74 0.17 SIDE CHAIN REMARK 500 5 ARG C 54 0.28 SIDE CHAIN REMARK 500 5 ARG C 72 0.21 SIDE CHAIN REMARK 500 6 ARG A 553 0.20 SIDE CHAIN REMARK 500 6 ARG A 564 0.23 SIDE CHAIN REMARK 500 6 ARG B 42 0.30 SIDE CHAIN REMARK 500 6 ARG B 54 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 91 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25657 RELATED DB: BMRB REMARK 900 RELATED ID: 2N3T RELATED DB: PDB REMARK 900 RELATED ID: 2N3U RELATED DB: PDB REMARK 900 RELATED ID: 2N3W RELATED DB: PDB DBREF 2N3V A 482 612 UNP P38764 RPN1_YEAST 482 612 DBREF 2N3V B 1 76 UNP P62987 RL40_HUMAN 1 76 DBREF 2N3V C 1 76 UNP P62987 RL40_HUMAN 1 76 SEQRES 1 A 131 ASP THR LYS ILE SER SER ALA ALA ILE LEU GLY LEU GLY SEQRES 2 A 131 ILE ALA PHE ALA GLY SER LYS ASN ASP GLU VAL LEU GLY SEQRES 3 A 131 LEU LEU LEU PRO ILE ALA ALA SER THR ASP LEU PRO ILE SEQRES 4 A 131 GLU THR ALA ALA MET ALA SER LEU ALA LEU ALA HIS VAL SEQRES 5 A 131 PHE VAL GLY THR CYS ASN GLY ASP ILE THR THR SER ILE SEQRES 6 A 131 MET ASP ASN PHE LEU GLU ARG THR ALA ILE GLU LEU LYS SEQRES 7 A 131 THR ASP TRP VAL ARG PHE LEU ALA LEU ALA LEU GLY ILE SEQRES 8 A 131 LEU TYR MET GLY GLN GLY GLU GLN VAL ASP ASP VAL LEU SEQRES 9 A 131 GLU THR ILE SER ALA ILE GLU HIS PRO MET THR SER ALA SEQRES 10 A 131 ILE GLU VAL LEU VAL GLY SER CYS ALA TYR THR GLY THR SEQRES 11 A 131 GLY SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HELIX 1 1 LYS A 484 PHE A 497 1 14 HELIX 2 2 ASP A 503 ALA A 513 1 11 HELIX 3 3 PRO A 519 PHE A 534 1 16 HELIX 4 4 ASN A 539 ARG A 553 1 15 HELIX 5 5 TRP A 562 LEU A 573 1 12 HELIX 6 6 GLU A 579 ILE A 591 1 13 HELIX 7 7 THR A 596 CYS A 606 1 11 HELIX 8 8 THR B 22 GLU B 34 1 13 HELIX 9 9 PRO B 37 GLN B 41 5 5 HELIX 10 10 THR C 22 GLU C 34 1 13 HELIX 11 11 PRO C 37 GLN C 41 5 5 SHEET 1 A 5 THR B 12 GLU B 16 0 SHEET 2 A 5 GLN B 2 THR B 7 -1 N ILE B 3 O LEU B 15 SHEET 3 A 5 THR B 66 VAL B 70 1 O LEU B 67 N PHE B 4 SHEET 4 A 5 ARG B 42 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 A 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 B 4 LYS C 11 GLU C 16 0 SHEET 2 B 4 GLN C 2 THR C 7 -1 N ILE C 3 O LEU C 15 SHEET 3 B 4 THR C 66 VAL C 70 1 O LEU C 67 N PHE C 4 SHEET 4 B 4 ARG C 42 ILE C 44 -1 N ILE C 44 O HIS C 68 LINK NZ LYS B 48 C GLY C 76 1555 1555 1.33 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000